Updated 5/7/25 by K. Lenderman - all code up to date & graphs generated - commented out outputs for winter sampling
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Attaching package: ‘dplyr’
The following objects are masked from ‘package:plyr’:
arrange, count, desc, failwith, id, mutate, rename, summarise, summarize
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Loading required package: lattice
Attaching package: ‘lubridate’
The following objects are masked from ‘package:base’:
date, intersect, setdiff, union
Attaching package: ‘purrr’
The following object is masked from ‘package:plyr’:
compact
Attaching package: ‘tidyr’
The following object is masked from ‘package:reshape2’:
smiths
#data_all <- list.files(path = "Lab_Data_TissueProcessing/raw_data/Files_by_Month", # Identify all CSV files
# pattern = "*.csv", full.names = TRUE) %>%
#lapply(read_csv) %>% # Store all files in list
# bind_rows # Combine data sets into one data set
#data_all # Print data to RStudio console
#as.data.frame(data_all) # Convert tibble to data.frame
#Filtering NAs and unnecessary columns
#data_all <- data_all %>% filter(!is.na(date_collected))
#data_all <- select(data_all, -light_regime, -oyster_zone)
#write.csv(data_all, "Master_files/tissue_processing_all_data.csv", row.names=FALSE)
##### USE THIS CODE TO MERGE DATA FILES - some of the files have columns that are not the same format (dates specifically), which was causing issues in merging. This code below should solve that problem. It converts all date columns to dates and m/d/y format #####
file_paths <- list.files(path = "Lab_Data_TissueProcessing/raw_data/Files_by_Month",
pattern = "*.csv", full.names = TRUE)
data_all <- lapply(file_paths, function(file_path) {
read_csv(file_path) %>%
mutate(
date_collected = as.Date(date_collected,format = "%m/%d/%Y"),
date_processed = as.Date(date_processed,format = "%m/%d/%Y"),
date_davidsons = as.Date(date_davidsons,format = "%m/%d/%Y"),
date_etoh = as.Date(date_etoh,format = "%m/%d/%Y")
)
}) %>%
bind_rows
New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 38 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (8): lab_id, date_collected, site, date_processed, condition, sample_notes, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (7): mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (4): lab_id, site, oyster_zone, condition
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (20): light_regime, dissection_notes, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24...
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (6): lab_id, site, oyster_zone, light_regime, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (18): mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ...25, ...26, ...27, ...28, .....
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 27── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (18): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17, ...18, ...19, ...20, ...21, ...22, .....
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 27── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (18): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17, ...18, ...19, ...20, ...21, ...22, .....
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (5): lab_id, site, oyster_zone, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (19): light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ...25, ...26, .....
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (6): lab_id, site, oyster_zone, light_regime, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (18): mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ...25, ...26, ...27, ...28, .....
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (4): lab_id, site, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (20): oyster_zone, light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ......
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (4): lab_id, site, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (20): oyster_zone, light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ......
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 27── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (18): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17, ...18, ...19, ...20, ...21, ...22, .....
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 35 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 46 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (8): lab_id, date_collected, site, date_processed, condition, sample_notes, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (7): mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (5): lab_id, site, oyster_zone, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (19): light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ...25, ...26, .....
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (6): lab_id, site, oyster_zone, light_regime, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (19): mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, date_etoh, ...21, ...22, ...23, ...24, ...25, ...26, ...27...
date (3): date_collected, date_processed, date_davidsons
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (4): lab_id, site, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (20): oyster_zone, light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ......
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (4): lab_id, site, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (20): oyster_zone, light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ......
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 27── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (8): lab_id, date_collected, site, date_processed, condition, sample_notes, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (17): mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17, ...18, ...19, ...20, ...21, ...22, ...23, ...24, .....
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (8): lab_id, date_collected, site, date_processed, condition, sample_notes, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (7): mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (5): lab_id, site, oyster_zone, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (19): light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ...25, ...26, .....
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 998 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (6): lab_id, site, oyster_zone, light_regime, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (19): mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, date_etoh, ...21, ...22, ...23, ...24, ...25, ...26, ...27...
date (3): date_collected, date_processed, date_davidsons
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (4): lab_id, site, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (21): oyster_zone, light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, date_etoh, ...21, ...22, ...23,...
date (3): date_collected, date_processed, date_davidsons
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (4): lab_id, site, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (21): oyster_zone, light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, date_etoh, ...21, ...22, ...23,...
date (3): date_collected, date_processed, date_davidsons
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (8): lab_id, date_collected, site, date_processed, condition, sample_notes, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (7): mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (8): lab_id, date_collected, site, date_processed, condition, sample_notes, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (7): mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (8): lab_id, date_collected, site, date_processed, condition, sample_notes, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (7): mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (5): lab_id, site, oyster_zone, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (19): light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ...25, ...26, .....
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (6): lab_id, site, oyster_zone, light_regime, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (19): mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, date_etoh, ...21, ...22, ...23, ...24, ...25, ...26, ...27...
date (3): date_collected, date_processed, date_davidsons
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (4): lab_id, site, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (21): oyster_zone, light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, date_etoh, ...21, ...22, ...23,...
date (3): date_collected, date_processed, date_davidsons
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (4): lab_id, site, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (21): oyster_zone, light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, date_etoh, ...21, ...22, ...23,...
date (3): date_collected, date_processed, date_davidsons
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (5): lab_id, site, oyster_zone, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (19): light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ...25, ...26, .....
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (6): lab_id, site, oyster_zone, light_regime, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (18): mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ...25, ...26, ...27, ...28, .....
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (4): lab_id, site, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (20): oyster_zone, light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ......
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (4): lab_id, site, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (20): oyster_zone, light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ......
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (8): lab_id, date_collected, site, date_processed, condition, sample_notes, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (7): mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (5): lab_id, site, oyster_zone, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (19): light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ...25, ...26, .....
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (6): lab_id, site, oyster_zone, light_regime, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (18): mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ...25, ...26, ...27, ...28, .....
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 36 Columns: 20── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (4): lab_id, site, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (7): oyster_zone, light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (4): lab_id, site, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (20): oyster_zone, light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ......
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (5): lab_id, site, oyster_zone, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (19): light_regime, mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ...25, ...26, .....
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 33── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (6): lab_id, site, oyster_zone, light_regime, condition, dissection_notes
dbl (5): lab_sample, ww_total_g, height_mm, length_mm, width_mm
lgl (18): mantle_rftm, ggr1_etoh, ggr2_etoh, adductor_etoh, cross_histology, ...21, ...22, ...23, ...24, ...25, ...26, ...27, ...28, .....
date (4): date_collected, date_processed, date_davidsons, date_etoh
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 27── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (8): lab_id, date_collected, site, date_processed, condition, sample_notes, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (17): mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17, ...18, ...19, ...20, ...21, ...22, ...23, ...24, .....
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (8): lab_id, date_collected, site, date_processed, condition, sample_notes, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (7): mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 36 Columns: 17── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (7): lab_id, date_collected, site, date_processed, condition, date_davidsons, date_etoh
dbl (2): lab_sample, height_mm
lgl (8): sample_notes, mantle_rftm, ggr1_frozen, ggr2_etoh, cross_histology, ...15, ...16, ...17
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
as.data.frame(data_all) # Convert tibble to data.frame
data_all <- data_all %>% filter(!is.na(date_collected))
data_all <- select(data_all, -light_regime, -oyster_zone)
View(data_all)
write.csv(data_all, "Master_files/tissue_processing_all_data.csv", row.names=FALSE)
#A wrong value caliper input was identified for the height of sample 0923GOLD_23. This code is removing that value from the data set as we cannot conclude what this original value was. The value is 8.62. This will cause this individual to fall out of the dataset when standardized to length. This code does not completely remove the individual from the dataset.
data_all$height_mm[data_all$height_mm == "0"] <- NA
data_all <- data_all %>% dplyr::mutate(date_collected= as.Date(date_collected), month = month(date_collected))
data_all <- data_all %>% dplyr::mutate(date_collected= as.Date(date_collected), year = year(date_collected))
#changing numeric month to month name
data_all$month <- factor(data_all$month, levels = c("1","2","3","4","5","6","7", "8", "9", "10", "11", "12"),
labels=c("Jan","Feb", "March","April","May", "June", "July", "Aug", "Sept", "Oct", "Nov", "Dec"))
data_all
data_all<- data_all %>%
dplyr::mutate(condition_score = recode(condition, "1_very_good" = 1, "2_good" = 2, "3_good_minus"= 3, "4_fair_plus"= 4, "5_fair"= 5,"6_fair_minus"=6,"7_poor_plus"=7, "8_poor"= 8, "9_very_poor"= 9))
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `condition_score = recode(...)`.
Caused by warning:
! Unreplaced values treated as NA as `.x` is not compatible.
Please specify replacements exhaustively or supply `.default`.
head(data_all)
NA
NA
#This chunk of code is removing 0723LAUR_20 and 0723LAUR_26 from the datasheet as they have been identified as spat on shell to avoid bias in the data. During this sample collection there were animals that were significantly smaller than the single set oysters. These individuals should be removed from all monthly sampling related datasheets including disease analysis. All tissue amples will be disgarded.
data_all <- data_all %>%
subset(lab_id != "0723LAUR_20") %>%
subset(lab_id != "0723LAUR_26")
data_all
NA
st_height <- summarySE(data_all%>% filter(!is.na(height_mm)), measurevar="height_mm", groupvars=c("site", "date_collected"))
st_height
#Calculate completeness for QC
st_height$Completeness <- st_height$N /30
st_height
write.csv(st_height, "Lab_Data_TissueProcessing/output\\Completeness_tissue_processing_data.csv", row.names=FALSE)
#Mean Height
ggplot(data=data_all, aes(x=site, y=height_mm, fill=site)) +
geom_boxplot()+ #scale_fill_manual(values=c("forestgreen","orange", "purple"))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title="Mean Shell Height ", x ="site", y = "Mean Shell Height (mm)") + facet_wrap(.~year)
#Body condition
ggplot(data=data_all, aes(x=site, y=condition_score, fill=site)) +
geom_boxplot()+ #scale_fill_manual(values=c("forestgreen","orange", "purple"))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title="Mean Condition Score ", x ="site", y = "Mean Body Condition Score")+ scale_y_reverse()+ facet_wrap(.~year)
mean_body_condition <- data_all %>%
dplyr::group_by(site, month, year)%>%
dplyr::summarize(mean_bsc = mean(condition_score, na.rm = TRUE))
`summarise()` has grouped output by 'site', 'month'. You can override using the `.groups` argument.
mean_body_condition
#for overlay graph
#mean_bcs_ashc <- mean_body_condition %>%
#filter(site == "ASHC") %>%
#filter(year == "2024")
#Mean body condtion scores - 2023
data_2023 <- data_all%>% filter(year=="2023")
ggplot(data=data_2023, aes(x=month, y=condition_score, group = month, fill = site)) +
geom_boxplot()+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
theme(axis.text.x = element_text(angle = -35, vjust = 0.5, hjust=1))+
labs(title="Mean Condition Score - 2023", x ="month", y = "Mean Body Condition Score")+ scale_y_reverse()+facet_wrap(~site)
#Mean body condtion scores - 2024
data_2024 <- data_all%>% filter(year=="2024")
ggplot(data=data_2024, aes(x=month, y=condition_score, group = month, fill = site)) +
geom_boxplot()+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
theme(axis.text.x = element_text(angle = -35, vjust = 0.5, hjust=1))+
labs(title="Mean Condition Score - 2024", x ="month", y = "Mean Body Condition Score")+ scale_y_reverse()+facet_wrap(~site)
#Mean body condition scores - 2025
data_2025 <- data_all%>% filter(year=="2025")
ggplot(data=data_2025, aes(x=month, y=condition_score, group = month, fill = site)) +
geom_boxplot()+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
theme(axis.text.x = element_text(angle = -35, vjust = 0.5, hjust=1))+
labs(title="Mean Condition Score - 2025", x ="month", y = "Mean Body Condition Score")+ scale_y_reverse()+facet_wrap(~site)
#Proportions graph Body condition scores
#Proportions graph Body condition scores - 2023
df_BCS_proportions2023<- data_2023 %>%
mutate(condition_score_numeric = as.numeric(condition_score),condition_score_bin = case_when(condition_score == 1 ~ "1", condition_score == 2 ~"2",condition_score == 3 ~ "3", condition_score == 4 ~"4",condition_score == 5 ~ "5", condition_score == 6 ~"6",condition_score == 7 ~ "7", condition_score == 8 ~"8", condition_score ==9 ~"9", TRUE ~ as.character(condition_score))) %>%
group_by(site, month, year, condition_score_bin) %>% dplyr ::summarise(Count= n()) %>%
ungroup() %>%
mutate(Proportion = Count/sum(Count))
`summarise()` has grouped output by 'site', 'month', 'year'. You can override using the `.groups` argument.
df_BCS_proportions2023<- na.omit(df_BCS_proportions2023)
BCS_proportion_all_2023<- ggplot(data=df_BCS_proportions2023, aes(x=month, y= Proportion, fill=condition_score_bin)) +
geom_bar(width = .5, stat="identity", position = "fill", colour = "black")+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))+
labs(title="Proportion of body condition scores - 2023", x ="month", y = "Proportion of body condition scores ")+ theme(axis.title.y = element_text(size = rel(1.3), angle =90), axis.title.x = element_text(size = rel(1.3), angle = 0))+
theme(axis.text=element_text(size=12))+
scale_fill_brewer(palette = "Blues", direction = -1)+
facet_wrap(~ site)
BCS_proportion_all_2023
#pdf(paste0(path = "Lab_Data_TissueProcessing/output" ,"/all_BCS_proportion_2023.pdf"), height = 7, width = 13)
#print(BCS_proportion_all_2023)
#dev.off()
#Proportions graph Body condition scores - 2024
df_BCS_proportions2024<- data_2024 %>%
mutate(condition_score_numeric = as.numeric(condition_score),condition_score_bin = case_when(condition_score == 1 ~ "1", condition_score == 2 ~"2",condition_score == 3 ~ "3", condition_score == 4 ~"4",condition_score == 5 ~ "5", condition_score == 6 ~"6",condition_score == 7 ~ "7", condition_score == 8 ~"8", condition_score ==9 ~"9", TRUE ~ as.character(condition_score))) %>%
group_by(site, month, year, condition_score_bin) %>% dplyr ::summarise(Count= n()) %>%
ungroup() %>%
mutate(Proportion = Count/sum(Count))
`summarise()` has grouped output by 'site', 'month', 'year'. You can override using the `.groups` argument.
df_BCS_proportions2024<- na.omit(df_BCS_proportions2024)
BCS_proportion_all_2024<- ggplot(data=df_BCS_proportions2024, aes(x=month, y= Proportion, fill=condition_score_bin)) +
geom_bar(width = .5, stat="identity", position = "fill", colour = "black")+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))+
labs(title="Proportion of body condition scores - 2024", x ="month", y = "Proportion of body condition scores ")+ theme(axis.title.y = element_text(size = rel(1.3), angle =90), axis.title.x = element_text(size = rel(1.3), angle = 0))+
theme(axis.text=element_text(size=12))+
scale_fill_brewer(palette = "Blues", direction = -1)+
facet_wrap(~ site)
BCS_proportion_all_2024
#pdf(paste0(path = "Lab_Data_TissueProcessing/output" ,"/all_BCS_proportion_2024.pdf"), height = 7, width = 13)
#print(BCS_proportion_all_2024)
#dev.off()
#Proportions graph Body condition scores - 2025
df_BCS_proportions2025<- data_2025 %>%
mutate(condition_score_numeric = as.numeric(condition_score),condition_score_bin = case_when(condition_score == 1 ~ "1", condition_score == 2 ~"2",condition_score == 3 ~ "3", condition_score == 4 ~"4",condition_score == 5 ~ "5", condition_score == 6 ~"6",condition_score == 7 ~ "7", condition_score == 8 ~"8", condition_score ==9 ~"9", TRUE ~ as.character(condition_score))) %>%
group_by(site, month, year, condition_score_bin) %>% dplyr ::summarise(Count= n()) %>%
ungroup() %>%
mutate(Proportion = Count/sum(Count))
`summarise()` has grouped output by 'site', 'month', 'year'. You can override using the `.groups` argument.
df_BCS_proportions2025<- na.omit(df_BCS_proportions2025)
BCS_proportion_all_2025<- ggplot(data=df_BCS_proportions2025, aes(x=month, y= Proportion, fill=condition_score_bin)) +
geom_bar(width = .5, stat="identity", position = "fill", colour = "black")+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))+
labs(title="Proportion of body condition scores - 2025", x ="month", y = "Proportion of body condition scores ")+ theme(axis.title.y = element_text(size = rel(1.3), angle =90), axis.title.x = element_text(size = rel(1.3), angle = 0))+
theme(axis.text=element_text(size=12))+
scale_fill_brewer(palette = "Blues", direction = -1)+
facet_wrap(~ site)#, scales = "free")
BCS_proportion_all_2025
pdf(paste0(path = "Lab_Data_TissueProcessing/output" ,"/all_BCS_proportion_2025.pdf"), height = 7, width = 13)
print(BCS_proportion_all_2025)
dev.off()
png
2
#Winter sampling
# winter_bcs <- rbind(df_BCS_proportions2024, df_BCS_proportions2025)
#
# winter_bcs <- winter_bcs %>% filter(month == "Dec"|month == "Jan"|month == "Feb")
#
# BCS_proportion_winter<- ggplot(data=winter_bcs, aes(x=factor (month, level=c('Dec', 'Jan', 'Feb')), y= Proportion, fill=condition_score_bin)) +
# geom_bar(width = .5, stat="identity", position = "fill", colour = "black")+
# theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
# theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))+
# labs(title="Proportion of body condition scores - Winter Sampling 2024-2025", x ="Month", y = "Proportion of body condition scores ")+ theme(axis.title.y = element_text(size = rel(1.3), angle =90), axis.title.x = element_text(size = rel(1.3), angle = 0))+
# theme(axis.text=element_text(size=12))+
# scale_fill_brewer(palette = "Blues", direction = -1)+
# facet_wrap(~ site)
#
# BCS_proportion_winter
# Proportion per month of intensity scores at three sites during 2023 & 2024 & 2025
df_bcs_proportions_new <- rbind(df_BCS_proportions2023, df_BCS_proportions2024, df_BCS_proportions2025)
df_bcs_proportions_new<- df_bcs_proportions_new %>% filter(!site=="LAUR")
ggplot(data=df_bcs_proportions_new, aes(x=month, y= Proportion, fill=condition_score_bin)) +
geom_bar(width = .5, stat="identity", position = "fill",colour = "black")+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))+
labs(fill ="Body condition scores")+
labs(title="Proportion of body condition scores", x ="month", y = "Proportion")+ theme(axis.title.y = element_text(size = rel(1.3), angle =90), axis.title.x = element_text(size = rel(1.3), angle = 0))+
theme(axis.text=element_text(size=12))+
scale_fill_brewer(palette = "Blues", direction = -1)+
#scale_x_continuous("Month", breaks = c(3,4,5,6,7,8,9,10))+
facet_grid(year ~site)
#Shell Pathology - all data #Includes 2023 data and all data that is in the 2024 format
shell_path <- list.files(path = "Lab_Data_TissueProcessing/raw_data/shell_pathology", # Identify all CSV files
pattern = "*.csv", full.names = TRUE) %>%
lapply(read_csv) %>% # Store all files in list
bind_rows # Combine data sets into one data set
Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, pathology_notes
lgl (12): boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolora...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, pathology_notes
lgl (12): boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolora...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 26── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, pathology_notes
lgl (24): boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discoloration, horn_add, ...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 26── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, pathology_notes
lgl (24): boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discoloration, horn_add, ...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, pathology_notes
lgl (12): boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolora...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 26── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (25): pathology_notes, boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolor...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 26── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (25): pathology_notes, boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolor...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 26── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (25): pathology_notes, boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolor...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolor...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 26── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (25): pathology_notes, boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolor...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 45 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolor...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, pathology_notes
lgl (12): boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolora...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, pathology_notes
lgl (12): boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolora...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolor...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolor...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, pathology_notes
lgl (12): boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discoloration, horn_add, ...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, pathology_notes
lgl (12): boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolora...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolor...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 15── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (14): pathology_notes, boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolor...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 28 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolor...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, pathology_notes
lgl (12): boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolora...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 30 Columns: 15── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, ...15
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolor...
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ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolor...
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ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolor...
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ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
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ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (13): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, pathology_notes
lgl (12): boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolora...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, pathology_notes
lgl (12): boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolora...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, pathology_notes
lgl (12): boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolora...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.New names:Rows: 999 Columns: 26── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): lab_id
lgl (25): pathology_notes, boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_dig...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, pathology_notes
lgl (12): boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolora...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 30 Columns: 14── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, pathology_notes
lgl (12): boring_sponge, shell_scarring, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, pale_digestive, discolora...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Rows: 838 Columns: 11── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): lab_id, pathology_notes
lgl (9): boring_sponge, polydora, conchiolin_mod_severe, mud_blister, pea_crab, gill_erosion, horn_add, shell_scarring, cyst_abscess
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
shell_path <- shell_path %>% filter(!is.na(lab_id))
shell_path <- shell_path %>% select(-c("...14":"...26"))
write.csv(shell_path, "Master_files/shell_pathology_all_data.csv", row.names=FALSE)
#Writing summary for shell pathology
shell_path_summary <- shell_path%>% separate(lab_id, c('Date_Site', 'ID'))
shell_path_summary <- select(shell_path_summary, -c("pathology_notes","ID",))
shell_path_summary$boring_sponge <- as.integer(as.logical(shell_path_summary$boring_sponge))
shell_path_summary$polydora <- as.integer(as.logical(shell_path_summary$polydora))
shell_path_summary$conchiolin_mod_severe <- as.integer(as.logical(shell_path_summary$conchiolin_mod_severe))
shell_path_summary$mud_blister <- as.integer(as.logical(shell_path_summary$mud_blister))
shell_path_summary$pea_crab <- as.integer(as.logical(shell_path_summary$pea_crab))
shell_path_summary$gill_erosion <- as.integer(as.logical(shell_path_summary$gill_erosion))
shell_path_summary$pale_digestive <- as.integer(as.logical(shell_path_summary$pale_digestive))
shell_path_summary$discoloration <- as.integer(as.logical(shell_path_summary$discoloration))
shell_path_summary$horn_add <- as.integer(as.logical(shell_path_summary$horn_add))
shell_path_summary$cyst_abscess <- as.integer(as.logical(shell_path_summary$cyst_abscess))
shell_path_summary$tumor <- as.integer(as.logical(shell_path_summary$tumor))
shell_path_summary$oyster_drill <- as.integer(as.logical(shell_path_summary$oyster_drill))
shell_path_summary$boring_snail <- as.integer(as.logical(shell_path_summary$boring_snail))
shell_path_summary$shell_scarring <- as.integer(as.logical(shell_path_summary$shell_scarring))
shell_path_count<- shell_path_summary %>%
dplyr::group_by(Date_Site) %>%
dplyr::summarize(Sample_count = n(),
Boring_sponge =sum(boring_sponge),
Polydora = sum(polydora),
Conchiolin =sum(conchiolin_mod_severe),
Mud_blister =sum(mud_blister),
Pea_crab =sum(pea_crab),
Gill_erosion =sum(gill_erosion),
Pale_digestive =sum(pale_digestive),
Discoloration =sum(discoloration),
Horn =sum(horn_add),
Cyst =sum(cyst_abscess),
Tumor =sum(tumor),
Oyster_drill =sum(oyster_drill),
Boring_snail =sum(boring_snail),
Shell_scarring =sum(shell_scarring),
Pathogen_count = sum(boring_sponge,polydora,conchiolin_mod_severe, mud_blister, pea_crab,
gill_erosion, pale_digestive, discoloration, horn_add, cyst_abscess,
tumor, oyster_drill, boring_snail, shell_scarring, na.rm = TRUE)) %>%
ungroup()
write.csv(shell_path_count, "Lab_Data_TissueProcessing/output/shell_pathology_counts.csv", row.names=FALSE)
shell_path_summary
df_ASHC<- data_all%>%
filter(site=="ASHC")
df_ASHC
## Shell Height ##
st_height_ASHC <- summarySE(df_ASHC, measurevar="height_mm", groupvars=c("date_collected"))
st_height_ASHC
## Body Condition ##
#Excludes April and May due to scoring change. These months are scored categorically 'fat, medium, watery'.
st_condition_ASHC<- summarySE(df_ASHC, measurevar = "condition_score", groupvars = c("date_collected"))
st_condition_ASHC
mean_condition_ASHC <- st_condition_ASHC %>%
filter(!is.na(condition_score)) %>% # Filter out rows where condition_score is NA
summarize(mean_bcs = mean(condition_score, na.rm = TRUE))
mean_condition_ASHC
NA
ggplot(data=df_ASHC, aes(x=month, y=height_mm, group= month)) +
geom_boxplot()+ #scale_fill_manual(values=c("forestgreen","orange", "purple"))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title=" Ash Creek Mean Shell Height ", x ="month", y = "Mean Shell Height (mm)")+facet_wrap(.~year)
#Condition distribution across all sample months - 2023
df_ASHC_2023 <- df_ASHC%>% filter(!year=="2024")
ASHC_BCS_dist2023 <-ggplot(data=df_ASHC_2023, aes(x= condition)) +
geom_bar()+ #scale_fill_manual(values=c("forestgreen","orange", "purple"))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title="Ash Creek Body Condition Score - 2023", x ="Condition categorization")+
facet_wrap(~ month, scales = "free")
ASHC_BCS_dist2023
#pdf(paste0(path = "Lab_Data_TissueProcessing/output" ,"/ASHC_BCS_dist_2023.pdf"), height = 7, width = 13)
#print(ASHC_BCS_dist2023)
#dev.off()
#Condition distribution across all sample months - 2024
df_ASHC_2024 <- df_ASHC%>% filter(!year=="2023")
ASHC_BCS_dist2024 <-ggplot(data=df_ASHC_2024, aes(x= condition)) +
geom_bar()+ #scale_fill_manual(values=c("forestgreen","orange", "purple"))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title="Ash Creek Body Condition Score - 2024", x ="Condition categorization")+
facet_wrap(~ month, scales = "free")
ASHC_BCS_dist2024
#pdf(paste0(path = "Lab_Data_TissueProcessing/output" ,"/ASHC_BCS_dist_2024.pdf"), height = 7, width = 13)
#print(ASHC_BCS_dist2024)
#dev.off()
#Condition distribution across all sample months - 2025
df_ASHC_2025 <- df_ASHC%>% filter(year=="2025")
ASHC_BCS_dist2025 <-ggplot(data=df_ASHC_2025, aes(x= condition)) +
geom_bar()+ #scale_fill_manual(values=c("forestgreen","orange", "purple"))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title="Ash Creek Body Condition Score - 2025", x ="Condition categorization")+
facet_wrap(~ month, scales = "free")
ASHC_BCS_dist2025
pdf(paste0(path = "Lab_Data_TissueProcessing/output" ,"/ASHC_BCS_dist_2025.pdf"), height = 7, width = 13)
print(ASHC_BCS_dist2025)
dev.off()
png
2
#Mean Body condition per month
ggplot(data=df_ASHC, aes(x= month, y= condition_score, group = month)) +
geom_boxplot()+ #scale_fill_manual(values=c("forestgreen","orange", "purple"))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title="Ash Creek Mean Body Condition Score ", x ="month", y= " condition score (1-9)") + scale_y_reverse()+facet_wrap(.~year)
#ASHC Proportions graph Body condition scores - all years
ASHC_BCS_proportions<- df_ASHC %>%
mutate(condition_score_numeric = as.numeric(condition_score),condition_score_bin = case_when(condition_score == 1 ~ "1", condition_score == 2 ~"2",condition_score == 3 ~ "3", condition_score == 4 ~"4",condition_score == 5 ~ "5", condition_score == 6 ~"6",condition_score == 7 ~ "7", condition_score == 8 ~"8", condition_score ==9 ~"9", TRUE ~ as.character(condition_score))) %>%
group_by(site, month, condition_score_bin, year) %>% dplyr::summarise(Count= n()) %>%
ungroup() %>%
mutate(Proportion = Count/sum(Count))
`summarise()` has grouped output by 'site', 'month', 'condition_score_bin'. You can override using the `.groups` argument.
ASHC_BCS_proportions<- na.omit(ASHC_BCS_proportions)
ASHC_BCS_proportions
BCS_proportion_ASHC<- ggplot(data=ASHC_BCS_proportions, aes(x=month, y= Proportion, fill=condition_score_bin)) +
geom_bar(width = .5, stat="identity", position = "fill")+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))+
labs(title="Ash Creek Proportion of body condition scores June- November", x ="month", y = "Proportion of body condition scores ")+ theme(axis.title.y = element_text(size = rel(1.3), angle =90), axis.title.x = element_text(size = rel(1.3), angle = 0))+
theme(axis.text=element_text(size=12))+
facet_wrap(~ year)
#scale_fill_brewer() +
#facet_wrap(~ site)
BCS_proportion_ASHC
pdf(paste0(path = "Lab_Data_TissueProcessing/output" ,"/ASHC_BCS_proportion.pdf"), height = 7, width = 13)
print(BCS_proportion_ASHC)
dev.off()
png
2
df_ASHC
ASHC_precent_greater_3 <- df_ASHC %>%
dplyr::group_by(month, site, year) %>%
dplyr::summarise(Percentage = mean(condition_score <= 3)*100)
`summarise()` has grouped output by 'month', 'site'. You can override using the `.groups` argument.
ASHC_precent_greater_3
ASHC_BCS_percentage <- ASHC_precent_greater_3%>%
#filter(year =="2024")%>%
ggplot(aes(x = month, y = Percentage)) +
#geom_bar(width = 0.5, stat = "identity", position = "fill") +
geom_col()+
theme_bw() +
theme(
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1),
axis.title.y = element_text(size = rel(1.3), angle = 90),
axis.title.x = element_text(size = rel(1.3), angle = 0),
axis.text = element_text(size = 12)
) +
labs(
title = "Ash Creek % of body condition scores >= 3",
x = "month",
y = "Percentage of body condition scores >= 3"
) +
facet_wrap(~year)
#scale_x_continuous( breaks = seq(5,12, by =1) )+
#ylim(0,60)+
#scale_y_continuous(limits = c(0,100), breaks = seq(0,100, by = 10))
ASHC_BCS_percentage
pdf(paste0(path = "Lab_Data_TissueProcessing/output", "/ASHC_BCS_percentage.pdf"),height = 7, width = 13)
print(ASHC_BCS_percentage)
dev.off()
png
2
df_FENC<- data_all%>%
filter(site=="FENC")
df_FENC
## Shell Height ##
st_height_FENC <- summarySE(df_FENC, measurevar="height_mm", groupvars=c("date_collected"))
st_height_FENC
## Body Condition ##
#Excludes April and May due to scoring change. These months are scored categorically 'fat, medium, watery'.
st_condition_FENC<- summarySE(df_FENC%>% filter(!is.na(condition_score)), measurevar = "condition_score", groupvars = c("date_collected"))
st_condition_FENC
NA
ggplot(data=df_FENC, aes(x=month, y=height_mm, group=month)) +
geom_boxplot()+ #scale_fill_manual(values=c("forestgreen","orange", "purple"))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title=" Fence Creek Mean Shell Height ", x ="month", y = "Mean Shell Height (mm)")+ facet_wrap(.~year)
#Condition distribution across all sample months - 2023
df_FENC.2023 <- df_FENC%>% filter(!year=="2024")
ggplot(data=df_FENC.2023, aes(x= condition)) +
geom_bar()+ #scale_fill_manual(values=c("forestgreen","orange", "purple"))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title="Fence Creek Body Condition index - 2023", x ="Condition categorization")+
facet_wrap(~ month, scales = "free")
#Condition distribution across all sample months - 2024
df_FENC.2024 <- df_FENC%>% filter(!year=="2023")
ggplot(data=df_FENC.2024, aes(x= condition)) +
geom_bar()+ #scale_fill_manual(values=c("forestgreen","orange", "purple"))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title="Fence Creek Body Condition index - 2024", x ="Condition categorization")+
facet_wrap(~ month, scales = "free")
#Mean Body condition per month
ggplot(data=df_FENC, aes(x= month, y= condition_score, group = month)) +
geom_boxplot()+ #scale_fill_manual(values=c("forestgreen","orange", "purple"))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title="Fence Creek Mean Body Condition Score", x ="month", y= " condition score (1-9)")+ scale_y_reverse() + facet_wrap(~ year, scales = "free")
#FENC Proportions graph Body condition scores - all years
FENC_BCS_proportions<- df_FENC %>%
mutate(condition_score_numeric = as.numeric(condition_score),condition_score_bin = case_when(condition_score == 1 ~ "1", condition_score == 2 ~"2",condition_score == 3 ~ "3", condition_score == 4 ~"4",condition_score == 5 ~ "5", condition_score == 6 ~"6",condition_score == 7 ~ "7", condition_score == 8 ~"8", condition_score ==9 ~"9", TRUE ~ as.character(condition_score))) %>%
group_by(site, month, condition_score_bin, year) %>% dplyr::summarise(Count= n()) %>%
ungroup() %>%
mutate(Proportion = Count/sum(Count))
`summarise()` has grouped output by 'site', 'month', 'condition_score_bin'. You can override using the `.groups` argument.
FENC_BCS_proportions<- na.omit(FENC_BCS_proportions)
FENC_BCS_proportions
BCS_proportion_FENC<- ggplot(data=FENC_BCS_proportions, aes(x=month, y= Proportion, fill=condition_score_bin)) +
geom_bar(width = .5, stat="identity", position = "fill")+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))+
labs(title="Fence Creek Proportion of body condition scores", x ="month", y = "Proportion of body condition scores ")+ theme(axis.title.y = element_text(size = rel(1.3), angle =90), axis.title.x = element_text(size = rel(1.3), angle = 0))+
theme(axis.text=element_text(size=12))+
facet_wrap(~ year)
#scale_fill_brewer() +
#facet_wrap(~ site)
BCS_proportion_FENC
pdf(paste0(path = "Lab_Data_TissueProcessing/output" ,"/FENC_BCS_proportion.pdf"), height = 7, width = 13)
print(BCS_proportion_FENC)
dev.off()
png
2
#removing 0823FENC_28 bcs was NA
df_FENC <- df_FENC %>% drop_na(condition)
FENC_precent_greater_3 <- df_FENC %>%
dplyr::group_by(month, year) %>%
dplyr::summarise(Percentage = mean(condition_score <= 3)*100)
`summarise()` has grouped output by 'month'. You can override using the `.groups` argument.
FENC_precent_greater_3
FENC_BCS_percentage <- ggplot(FENC_precent_greater_3,aes(x = month, y = Percentage)) +
#geom_bar(width = 0.5, stat = "identity", position = "fill") +
geom_col()+
theme_bw() +
theme(
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1),
axis.title.y = element_text(size = rel(1.3), angle = 90),
axis.title.x = element_text(size = rel(1.3), angle = 0),
axis.text = element_text(size = 12)
) +
labs(
title = "Fence Creek % of body condition scores >= 3",
x = "month",
y = "Percentage of body condition scores >= 3"
) +
facet_wrap(~year)
#scale_x_continuous( breaks = seq(5,12, by =1) )+
#ylim(0,60)+
#scale_y_continuous(limits = c(0,100), breaks = seq(0,100, by = 10))
FENC_BCS_percentage
pdf(paste0(path = "Lab_Data_TissueProcessing/output", "/FENC_BCS_percentage.pdf"),height = 7, width = 13)
print(FENC_BCS_percentage)
dev.off()
png
2
df_GOLD<- data_all%>%
filter(site=="GOLD")
df_GOLD <- df_GOLD %>% filter(!is.na(height_mm))
#2023 data
df_GOLD2023 <- df_GOLD%>% filter(!year=="2024")
#2024 data
df_GOLD2024 <- df_GOLD%>% filter(!year=="2023")
df_GOLD$height_mm<-as.numeric(df_GOLD$height_mm)
mean_shell_height <- df_GOLD %>% mutate(year = year(date_collected)) %>% group_by(year)%>% dplyr::summarise(mean_height = mean(height_mm)) #summarySE(measurevar="height_mm", groupvars=c("year"))
mean_shell_height
## Shell Height ##
st_height_GOLD <- summarySE(df_GOLD, measurevar="height_mm", groupvars=c("date_collected"))
st_height_GOLD
## Body Condition ##
st_condition_GOLD<- summarySE(df_GOLD, measurevar = "condition_score", groupvars = c("date_collected"))
st_condition_GOLD
NA
#GOLD Proportions graph Body condition scores
GOLD_BCS_proportions<- df_GOLD %>%
mutate(condition_score_numeric = as.numeric(condition_score),condition_score_bin = case_when(condition_score == 1 ~ "1", condition_score == 2 ~"2",condition_score == 3 ~ "3", condition_score == 4 ~"4",condition_score == 5 ~ "5", condition_score == 6 ~"6",condition_score == 7 ~ "7", condition_score == 8 ~"8", condition_score ==9 ~"9", TRUE ~ as.character(condition_score))) %>%
group_by(site, month, year, condition_score_bin) %>% dplyr::summarise(Count= n()) %>%
ungroup() %>%
mutate(Proportion = Count/sum(Count))
`summarise()` has grouped output by 'site', 'month', 'year'. You can override using the `.groups` argument.
GOLD_BCS_proportions<- na.omit(GOLD_BCS_proportions)
BCS_proportion_GOLD <- ggplot(data=GOLD_BCS_proportions, aes(x=month, y= Proportion, fill=condition_score_bin)) +
geom_bar(width = .5, stat="identity", position = "fill", colour = "black")+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))+
labs(title="Gold Star Beach Proportion of body condition scores", x ="month", y = "Proportion of body condition scores ")+ theme(axis.title.y = element_text(size = rel(1.3), angle =90), axis.title.x = element_text(size = rel(1.3), angle = 0))+
theme(axis.text=element_text(size=12))+
scale_fill_brewer(palette = "Blues", direction = -1)+
facet_wrap(~ year)
BCS_proportion_GOLD
pdf(paste0(path = "Lab_Data_TissueProcessing/output" ,"/GOLD_BCS_proportion.pdf"), height = 7, width = 13)
print(BCS_proportion_GOLD)
dev.off()
png
2
df_GOLD
GOLD_precent_greater_3 <- df_GOLD %>%
dplyr::group_by(month, site, year) %>%
dplyr::summarise(Percentage = mean(condition_score <= 3)*100)
`summarise()` has grouped output by 'month', 'site'. You can override using the `.groups` argument.
GOLD_precent_greater_3
GOLD_BCS_percentage <- GOLD_precent_greater_3 %>%
ggplot(aes(x = month, y = Percentage)) +
#geom_bar(width = 0.5, stat = "identity", position = "fill") +
geom_col()+
theme_bw() +
theme(
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1),
axis.title.y = element_text(size = rel(1.3), angle = 90),
axis.title.x = element_text(size = rel(1.3), angle = 0),
axis.text = element_text(size = 12)
) +
labs(
title = "Gold Star Beach % of body condition scores >= 3",
x = "month",
y = "Percentage of body condition scores >= 3"
) +facet_wrap(~year)
#+ scale_x_continuous( breaks = seq(5,12, by =1) )+
#ylim(0,60)+
#scale_y_continuous(limits = c(0,100), breaks = seq(0,100, by = 10))
GOLD_BCS_percentage
pdf(paste0(path = "Lab_Data_TissueProcessing/output", "/GOLD_BCS_percentage.pdf"),height = 7, width = 13)
print(GOLD_BCS_percentage)
dev.off()
png
2
ggplot(data=df_GOLD, aes(x=month, y=height_mm, group= month)) +
geom_boxplot()+ #scale_fill_manual(values=c("forestgreen","orange", "purple"))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title="Goldstar Beach Mean Shell Height ", x ="month", y = "Mean Shell Height (mm)") + #scale_x_continuous(limits= c(4,11), breaks = seq(5,10, by =1))+
geom_smooth(method = "lm", se = FALSE)+ facet_wrap(~year)
#Condition distribution across all sample months - 2023
ggplot(data=df_GOLD2023, aes(x= condition)) +
geom_bar()+ #scale_fill_manual(values=c("forestgreen","orange", "purple"))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title="Goldstar Beach Body Condition Score - 2023 ", x ="Condition categorization")+
facet_wrap(~ month, scales = "free")
#Condition distribution across all sample months - 2024
ggplot(data=df_GOLD2024, aes(x= condition)) +
geom_bar()+ #scale_fill_manual(values=c("forestgreen","orange", "purple"))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title="Goldstar Beach Body Condition Score - 2024", x ="Condition categorization")+
facet_wrap(~ month, scales = "free")
#Mean Body condition per month
ggplot(data=df_GOLD, aes(x= month, y= condition_score, group = month)) +
geom_boxplot()+ #scale_fill_manual(values=c("forestgreen","orange", "purple"))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
labs(title="Goldstar Beach Mean Body Condition Score ", x ="month", y= " condition score (1-9)")+ scale_y_reverse() + facet_wrap(~year)
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
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```r
df_LAUR<- data_all%>%
filter(site==\LAUR\)
## Shell Height ##
st_height_LAUR <- summarySE(df_LAUR, measurevar=\height_mm\, groupvars=c(\date_collected\))
st_height_LAUR
## Body Condition ##
## Excludes May due to scoring system change. May scored fat, medium, watery.
st_condition_LAUR<- summarySE(df_LAUR, measurevar = \condition_score\, groupvars = c(\date_collected\))
st_condition_LAUR
```
<!-- rnb-source-end -->
```r
df_LAUR<- data_all%>%
filter(site==\LAUR\)
## Shell Height ##
st_height_LAUR <- summarySE(df_LAUR, measurevar=\height_mm\, groupvars=c(\date_collected\))
st_height_LAUR
## Body Condition ##
## Excludes May due to scoring system change. May scored fat, medium, watery.
st_condition_LAUR<- summarySE(df_LAUR, measurevar = \condition_score\, groupvars = c(\date_collected\))
st_condition_LAUR
<!-- rnb-source-end -->
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ggplot(data=df_LAUR, aes(x=month, y=height_mm, group= month)) +
geom_boxplot()+ #scale_fill_manual(values=c(\forestgreen\,\orange\, \purple\))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title=\ Laurel Hollow Mean Shell Height - 2023\, x =\month\, y = \Mean Shell Height (mm)\)
<!-- rnb-output-end -->
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```r
```r
ggplot(data=df_LAUR, aes(x=month, y=height_mm, group= month)) +
geom_boxplot()+ #scale_fill_manual(values=c(\forestgreen\,\orange\, \purple\))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title=\ Laurel Hollow Mean Shell Height - 2023\, x =\month\, y = \Mean Shell Height (mm)\)
```
```
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#Condition distribution across all sample months
ggplot(data=df_LAUR, aes(x= condition)) +
geom_bar()+ #scale_fill_manual(values=c(\forestgreen\,\orange\, \purple\))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title=\Laurel Hollow Body Condition index - 2023\, x =\Condition categorization\)+
facet_wrap(~ month, scales = \free\)
#Mean Body condition per month
ggplot(data=df_LAUR, aes(x= month, y= condition_score, group = month)) +
geom_boxplot()+ #scale_fill_manual(values=c(\forestgreen\,\orange\, \purple\))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
labs(title=\Laurel Hollow Mean Body Condition Score - 2023\, x =\month\, y= \ condition score (1-9)\)+ scale_y_reverse()
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
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```r
```r
#Condition distribution across all sample months
ggplot(data=df_LAUR, aes(x= condition)) +
geom_bar()+ #scale_fill_manual(values=c(\forestgreen\,\orange\, \purple\))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
labs(title=\Laurel Hollow Body Condition index - 2023\, x =\Condition categorization\)+
facet_wrap(~ month, scales = \free\)
#Mean Body condition per month
ggplot(data=df_LAUR, aes(x= month, y= condition_score, group = month)) +
geom_boxplot()+ #scale_fill_manual(values=c(\forestgreen\,\orange\, \purple\))+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
labs(title=\Laurel Hollow Mean Body Condition Score - 2023\, x =\month\, y= \ condition score (1-9)\)+ scale_y_reverse()
#theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
```
```
<!-- rnb-source-end -->
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#LAUR Proportions graph Body condition scores - 2023 (only sampled one year)
<!-- rnb-text-end -->
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<!-- rnb-output-begin 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-->
LAUR_BCS_proportions<- df_LAUR %>%
mutate(condition_score_numeric = as.numeric(condition_score),condition_score_bin = case_when(condition_score == 1 ~ \1\, condition_score == 2 ~\2\,condition_score == 3 ~ \3\, condition_score == 4 ~\4\,condition_score == 5 ~ \5\, condition_score == 6 ~\6\,condition_score == 7 ~ \7\, condition_score == 8 ~\8\, condition_score ==9 ~\9\, TRUE ~ as.character(condition_score))) %>%
group_by(site, month, condition_score_bin, year) %>% dplyr::summarise(Count= n()) %>%
ungroup() %>%
mutate(Proportion = Count/sum(Count))
LAUR_BCS_proportions<- na.omit(LAUR_BCS_proportions)
LAUR_BCS_proportions
BCS_proportion_LAUR<- ggplot(data=LAUR_BCS_proportions, aes(x=month, y= Proportion, fill=condition_score_bin)) +
geom_bar(width = .5, stat=\identity\, position = \fill\)+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))+
labs(title=\Laurel Hollow Proportion of body condition scores - 2023\, x =\month\, y = \Proportion of body condition scores \)+ theme(axis.title.y = element_text(size = rel(1.3), angle =90), axis.title.x = element_text(size = rel(1.3), angle = 0))+
theme(axis.text=element_text(size=12))
#facet_wrap(~ year)
#scale_fill_brewer() +
#facet_wrap(~ site)
BCS_proportion_LAUR
pdf(paste0(path = \Lab_Data_TissueProcessing/output\ ,\/LAUR_BCS_proportion.pdf\), height = 7, width = 13)
print(BCS_proportion_LAUR)
dev.off()
<!-- rnb-output-end -->
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bmBgYFxuXG48IS0tIHJuYi1zb3VyY2UtZW5kIC0tPlxuIn0= -->
<!-- rnb-source-begin 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 -->
```r
```r
LAUR_BCS_proportions<- df_LAUR %>%
mutate(condition_score_numeric = as.numeric(condition_score),condition_score_bin = case_when(condition_score == 1 ~ \1\, condition_score == 2 ~\2\,condition_score == 3 ~ \3\, condition_score == 4 ~\4\,condition_score == 5 ~ \5\, condition_score == 6 ~\6\,condition_score == 7 ~ \7\, condition_score == 8 ~\8\, condition_score ==9 ~\9\, TRUE ~ as.character(condition_score))) %>%
group_by(site, month, condition_score_bin, year) %>% dplyr::summarise(Count= n()) %>%
ungroup() %>%
mutate(Proportion = Count/sum(Count))
LAUR_BCS_proportions<- na.omit(LAUR_BCS_proportions)
LAUR_BCS_proportions
BCS_proportion_LAUR<- ggplot(data=LAUR_BCS_proportions, aes(x=month, y= Proportion, fill=condition_score_bin)) +
geom_bar(width = .5, stat=\identity\, position = \fill\)+
theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))+
labs(title=\Laurel Hollow Proportion of body condition scores - 2023\, x =\month\, y = \Proportion of body condition scores \)+ theme(axis.title.y = element_text(size = rel(1.3), angle =90), axis.title.x = element_text(size = rel(1.3), angle = 0))+
theme(axis.text=element_text(size=12))
#facet_wrap(~ year)
#scale_fill_brewer() +
#facet_wrap(~ site)
BCS_proportion_LAUR
pdf(paste0(path = \Lab_Data_TissueProcessing/output\ ,\/LAUR_BCS_proportion.pdf\), height = 7, width = 13)
print(BCS_proportion_LAUR)
dev.off()
```
```
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<!-- rnb-text-begin -->
# % of scores >3 at LAUR june - november
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<!-- rnb-output-begin eyJkYXRhIjoiXG48IS0tIHJuYi1zb3VyY2UtYmVnaW4gZXlKa1lYUmhJam9pWUdCZ2NseHVYRzRqY21WdGIzWnBibWNnTURneU0wWkZUa05mTWpnZ1ltTnpJSGRoY3lCT1FWeHVaR1pmVEVGVlVpNGdQQzBnWkdaZlRFRlZVaVUrSldacGJIUmxjaWdoY205M1gyNTFiV0psY2lncElDVnBiaVVnWXlneUtTbGNibHh1VEVGVlVsOXdjbVZqWlc1MFgyZHlaV0YwWlhKZk15QThMU0JrWmw5TVFWVlNMaUFsUGlWY2JpQWdaSEJzZVhJNk9tZHliM1Z3WDJKNUtHMXZiblJvTENCemFYUmxMQ0I1WldGeUtTQWxQaVZjYmlBZ1pIQnNlWEk2T25OMWJXMWhjbWx6WlNoUVpYSmpaVzUwWVdkbElEMGdiV1ZoYmloamIyNWthWFJwYjI1ZmMyTnZjbVVnUEQwZ015a3FNVEF3S1Z4dVRFRlZVbDl3Y21WalpXNTBYMmR5WldGMFpYSmZNMXh1WEc1TVFWVlNYMEpEVTE5d1pYSmpaVzUwWVdkbElEd3RJRXhCVlZKZmNISmxZMlZ1ZEY5bmNtVmhkR1Z5WHpNZ0pUNGxYRzRnSUdkbmNHeHZkQ2hoWlhNb2VDQTlJRzF2Ym5Sb0xDQjVJRDBnVUdWeVkyVnVkR0ZuWlNrcElDdGNiaUFnSTJkbGIyMWZZbUZ5S0hkcFpIUm9JRDBnTUM0MUxDQnpkR0YwSUQwZ1hDSnBaR1Z1ZEdsMGVWd2lMQ0J3YjNOcGRHbHZiaUE5SUZ3aVptbHNiRndpS1NBclhHNGdJQ0FnWjJWdmJWOWpiMndvS1N0Y2JpQWdkR2hsYldWZlluY29LU0FyWEc0Z0lIUm9aVzFsS0Z4dUlDQWdJSEJoYm1Wc0xtZHlhV1F1YldGcWIzSWdQU0JsYkdWdFpXNTBYMkpzWVc1cktDa3NYRzRnSUNBZ2NHRnVaV3d1WjNKcFpDNXRhVzV2Y2lBOUlHVnNaVzFsYm5SZllteGhibXNvS1N4Y2JpQWdJQ0JoZUdsekxuUmxlSFF1ZUNBOUlHVnNaVzFsYm5SZmRHVjRkQ2hoYm1kc1pTQTlJRFExTENCMmFuVnpkQ0E5SURFc0lHaHFkWE4wSUQwZ01Ta3NYRzRnSUNBZ1lYaHBjeTUwYVhSc1pTNTVJRDBnWld4bGJXVnVkRjkwWlhoMEtITnBlbVVnUFNCeVpXd29NUzR6S1N3Z1lXNW5iR1VnUFNBNU1Da3NYRzRnSUNBZ1lYaHBjeTUwYVhSc1pTNTRJRDBnWld4bGJXVnVkRjkwWlhoMEtITnBlbVVnUFNCeVpXd29NUzR6S1N3Z1lXNW5iR1VnUFNBd0tTeGNiaUFnSUNCaGVHbHpMblJsZUhRZ1BTQmxiR1Z0Wlc1MFgzUmxlSFFvYzJsNlpTQTlJREV5S1Z4dUlDQXBJQ3RjYmlBZ2JHRmljeWhjYmlBZ0lDQjBhWFJzWlNBOUlGd2lSMjlzWkNCVGRHRnlJRUpsWVdOb0lDVWdiMllnWW05a2VTQmpiMjVrYVhScGIyNGdjMk52Y21WeklENDlJRE5jSWl4Y2JpQWdJQ0I0SUQwZ1hDSnRiMjUwYUZ3aUxGeHVJQ0FnSUhrZ1BTQmNJbEJsY21ObGJuUmhaMlVnYjJZZ1ltOWtlU0JqYjI1a2FYUnBiMjRnYzJOdmNtVnpJRDQ5SUROY0lseHVJQ0FwSUNNclptRmpaWFJmZDNKaGNDaCtlV1ZoY2lsY2JpQWdJeXNnYzJOaGJHVmZlRjlqYjI1MGFXNTFiM1Z6S0NCaWNtVmhhM01nUFNCelpYRW9OU3d4TWl3Z1lua2dQVEVwSUNrclhHNGdJQ041YkdsdEtEQXNOakFwS3lCY2JpQWdJM05qWVd4bFgzbGZZMjl1ZEdsdWRXOTFjeWhzYVcxcGRITWdQU0JqS0RBc01UQXdLU3dnWW5KbFlXdHpJRDBnYzJWeEtEQXNNVEF3TENCaWVTQTlJREV3S1NrZ1hHNWNiaUFnSUNCY2JreEJWVkpmUWtOVFgzQmxjbU5sYm5SaFoyVmNibHh1Y0dSbUtIQmhjM1JsTUNod1lYUm9JRDBnWENKTVlXSmZSR0YwWVY5VWFYTnpkV1ZRY205alpYTnphVzVuTDI5MWRIQjFkRndpTENCY0lpOU1RVlZTWDBKRFUxOXdaWEpqWlc1MFlXZGxMbkJrWmx3aUtTeG9aV2xuYUhRZ1BTQTNMQ0IzYVdSMGFDQTlJREV6S1Z4dWNISnBiblFvVEVGVlVsOUNRMU5mY0dWeVkyVnVkR0ZuWlNsY2JtUmxkaTV2Wm1Zb0tTQmNibHh1WEc1Y2JtQmdZQ0o5IC0tPlxuXG5gYGByXG5cbiNyZW1vdmluZyAwODIzRkVOQ18yOCBiY3Mgd2FzIE5BXG5kZl9MQVVSLiA8LSBkZl9MQVVSJT4lZmlsdGVyKCFyb3dfbnVtYmVyKCkgJWluJSBjKDIpKVxuXG5MQVVSX3ByZWNlbnRfZ3JlYXRlcl8zIDwtIGRmX0xBVVIuICU+JVxuICBkcGx5cjo6Z3JvdXBfYnkobW9udGgsIHNpdGUsIHllYXIpICU+JVxuICBkcGx5cjo6c3VtbWFyaXNlKFBlcmNlbnRhZ2UgPSBtZWFuKGNvbmRpdGlvbl9zY29yZSA8PSAzKSoxMDApXG5MQVVSX3ByZWNlbnRfZ3JlYXRlcl8zXG5cbkxBVVJfQkNTX3BlcmNlbnRhZ2UgPC0gTEFVUl9wcmVjZW50X2dyZWF0ZXJfMyAlPiVcbiAgZ2dwbG90KGFlcyh4ID0gbW9udGgsIHkgPSBQZXJjZW50YWdlKSkgK1xuICAjZ2VvbV9iYXIod2lkdGggPSAwLjUsIHN0YXQgPSBcXGlkZW50aXR5XFwsIHBvc2l0aW9uID0gXFxmaWxsXFwpICtcbiAgICBnZW9tX2NvbCgpK1xuICB0aGVtZV9idygpICtcbiAgdGhlbWUoXG4gICAgcGFuZWwuZ3JpZC5tYWpvciA9IGVsZW1lbnRfYmxhbmsoKSxcbiAgICBwYW5lbC5ncmlkLm1pbm9yID0gZWxlbWVudF9ibGFuaygpLFxuICAgIGF4aXMudGV4dC54ID0gZWxlbWVudF90ZXh0KGFuZ2xlID0gNDUsIHZqdXN0ID0gMSwgaGp1c3QgPSAxKSxcbiAgICBheGlzLnRpdGxlLnkgPSBlbGVtZW50X3RleHQoc2l6ZSA9IHJlbCgxLjMpLCBhbmdsZSA9IDkwKSxcbiAgICBheGlzLnRpdGxlLnggPSBlbGVtZW50X3RleHQoc2l6ZSA9IHJlbCgxLjMpLCBhbmdsZSA9IDApLFxuICAgIGF4aXMudGV4dCA9IGVsZW1lbnRfdGV4dChzaXplID0gMTIpXG4gICkgK1xuICBsYWJzKFxuICAgIHRpdGxlID0gXFxHb2xkIFN0YXIgQmVhY2ggJSBvZiBib2R5IGNvbmRpdGlvbiBzY29yZXMgPj0gM1xcLFxuICAgIHggPSBcXG1vbnRoXFwsXG4gICAgeSA9IFxcUGVyY2VudGFnZSBvZiBib2R5IGNvbmRpdGlvbiBzY29yZXMgPj0gM1xcXG4gICkgIytmYWNldF93cmFwKH55ZWFyKVxuICAjKyBzY2FsZV94X2NvbnRpbnVvdXMoIGJyZWFrcyA9IHNlcSg1LDEyLCBieSA9MSkgKStcbiAgI3lsaW0oMCw2MCkrIFxuICAjc2NhbGVfeV9jb250aW51b3VzKGxpbWl0cyA9IGMoMCwxMDApLCBicmVha3MgPSBzZXEoMCwxMDAsIGJ5ID0gMTApKSBcblxuICAgIFxuTEFVUl9CQ1NfcGVyY2VudGFnZVxuXG5wZGYocGFzdGUwKHBhdGggPSBcXExhYl9EYXRhX1Rpc3N1ZVByb2Nlc3Npbmcvb3V0cHV0XFwsIFxcL0xBVVJfQkNTX3BlcmNlbnRhZ2UucGRmXFwpLGhlaWdodCA9IDcsIHdpZHRoID0gMTMpXG5wcmludChMQVVSX0JDU19wZXJjZW50YWdlKVxuZGV2Lm9mZigpIFxuXG5cblxuYGBgXG5cbjwhLS0gcm5iLXNvdXJjZS1lbmQgLS0+XG4ifQ== -->
#removing 0823FENC_28 bcs was NA
df_LAUR. <- df_LAUR%>%filter(!row_number() %in% c(2))
LAUR_precent_greater_3 <- df_LAUR. %>%
dplyr::group_by(month, site, year) %>%
dplyr::summarise(Percentage = mean(condition_score <= 3)*100)
LAUR_precent_greater_3
LAUR_BCS_percentage <- LAUR_precent_greater_3 %>%
ggplot(aes(x = month, y = Percentage)) +
#geom_bar(width = 0.5, stat = \identity\, position = \fill\) +
geom_col()+
theme_bw() +
theme(
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1),
axis.title.y = element_text(size = rel(1.3), angle = 90),
axis.title.x = element_text(size = rel(1.3), angle = 0),
axis.text = element_text(size = 12)
) +
labs(
title = \Gold Star Beach % of body condition scores >= 3\,
x = \month\,
y = \Percentage of body condition scores >= 3\
) #+facet_wrap(~year)
#+ scale_x_continuous( breaks = seq(5,12, by =1) )+
#ylim(0,60)+
#scale_y_continuous(limits = c(0,100), breaks = seq(0,100, by = 10))
LAUR_BCS_percentage
pdf(paste0(path = \Lab_Data_TissueProcessing/output\, \/LAUR_BCS_percentage.pdf\),height = 7, width = 13)
print(LAUR_BCS_percentage)
dev.off()
<!-- rnb-output-end -->
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```r
```r
#removing 0823FENC_28 bcs was NA
df_LAUR. <- df_LAUR%>%filter(!row_number() %in% c(2))
LAUR_precent_greater_3 <- df_LAUR. %>%
dplyr::group_by(month, site, year) %>%
dplyr::summarise(Percentage = mean(condition_score <= 3)*100)
LAUR_precent_greater_3
LAUR_BCS_percentage <- LAUR_precent_greater_3 %>%
ggplot(aes(x = month, y = Percentage)) +
#geom_bar(width = 0.5, stat = \identity\, position = \fill\) +
geom_col()+
theme_bw() +
theme(
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1),
axis.title.y = element_text(size = rel(1.3), angle = 90),
axis.title.x = element_text(size = rel(1.3), angle = 0),
axis.text = element_text(size = 12)
) +
labs(
title = \Gold Star Beach % of body condition scores >= 3\,
x = \month\,
y = \Percentage of body condition scores >= 3\
) #+facet_wrap(~year)
#+ scale_x_continuous( breaks = seq(5,12, by =1) )+
#ylim(0,60)+
#scale_y_continuous(limits = c(0,100), breaks = seq(0,100, by = 10))
LAUR_BCS_percentage
pdf(paste0(path = \Lab_Data_TissueProcessing/output\, \/LAUR_BCS_percentage.pdf\),height = 7, width = 13)
print(LAUR_BCS_percentage)
dev.off()
```
```
<!-- rnb-source-end -->
<!-- rnb-output-end -->
<!-- rnb-chunk-end -->
<!-- rnb-text-begin -->
<!-- rnb-text-end -->
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only 2023 data\ndata_2023 <- data_all%>%  filter(!year==\\2024\\)\n\ndf_BCS_proportions<- data_2023 %>%\n  mutate(condition_score_numeric = as.numeric(condition_score),condition_score_bin = case_when(condition_score == 1 ~ \\1\\, condition_score == 2 ~\\2\\,condition_score == 3 ~ \\3\\, condition_score == 4 ~\\4\\,condition_score == 5 ~ \\5\\, condition_score == 6 ~\\6\\,condition_score == 7 ~ \\7\\, condition_score == 8 ~\\8\\, condition_score ==9 ~\\9\\, TRUE ~ as.character(condition_score))) %>%\n  group_by(site, month, condition_score_bin) %>% dplyr ::summarise(Count= n()) %>%\n  ungroup() %>%\n  mutate(Proportion = Count/sum(Count))\n\ndf_BCS_proportions<- na.omit(df_BCS_proportions)\n\ndf_BCS_proportions$month <- factor(df_BCS_proportions$month, levels = c(\\5\\,\\6\\,\\7\\, \\8\\, \\9\\, \\10\\, \\11\\),\n        labels=c(\\May\\, \\June\\, \\July\\, \\Aug\\, \\Sept\\, \\Oct\\, \\Nov\\))\ndf_BCS_proportions$site <- factor(df_BCS_proportions$site, levels = c(\\ASHC\\,\\FENC\\,\\GOLD\\, \\LAUR\\),\n        labels=c(\\Ash Creek\\, \\Fence Creek\\, \\Gold Star\\, \\Laurel Hollow\\))\n\nbcs.prop.2023 <- ggplot(data=df_BCS_proportions, aes(x=month, y= Proportion, fill=condition_score_bin)) +\n  geom_bar(width = .5, stat=\\identity\\, position = \\fill\\, colour = \\black\\)+  \n   theme_bw() +  theme(panel.grid.minor = element_blank())+ \n  theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1, size = rel(.9)))+\n  theme(panel.grid.major.x =element_blank())+\n  labs(title=\\Body condition scores in 2023\\, x =\\Month\\, y = \\Proportion of body condition scores \\)+ theme(axis.title.y = element_text(size = rel(1.2), angle =90), axis.title.x = element_text(size = rel(1.2), angle = 0))+ scale_fill_brewer(palette = \\Blues\\) +\n  theme(strip.text = element_text(size = 15))+\n  theme (legend.title = element_text(size = 18))+\n  theme(title = element_text(size = 17))+\n  theme(axis.text=element_text(size=17))+\n  labs(fill =\\Body Condition Score\\)+\n  facet_wrap(~ site )\nbcs.prop.2023\n\n#pdf(paste0(path = \\Lab_Data_TissueProcessing/output\\ ,\\/BCS_proportion_2023.pdf\\), height = 7, width = 13)\n#print(bcs.prop.2023)\n#dev.off()\n\n#BCS_proportion_all+scale_fill_manual(values = c(\\#003C30\\,\\#01665E\\,\\#80CDC1\\,\\#C7EAE5\\,\\#F6E8C3\\,\\#DFC27D\\,\\#BF812D\\, \\#8C510A\\,\\#543005\\ ))\n#scale_fill_manual(values = c(\\#003C30\\,\\#01665E\\,\\#80CDC1\\,\\#C7EAE5\\,\\azure1\\,\\slategray1\\,\\slategray3\\, \\slategray4\\, \\gray25\\ )) \n\nf <- function(pal) brewer.pal(brewer.pal.info[pal, \\maxcolors\\], pal)\n(cols <- f(\\YlGnBu\\))\n```\n\n<!-- rnb-source-end -->\n"} -->
#Coding graphs for LIS Conference - only 2023 data
data_2023 <- data_all%>% filter(!year==\2024\)
df_BCS_proportions<- data_2023 %>%
mutate(condition_score_numeric = as.numeric(condition_score),condition_score_bin = case_when(condition_score == 1 ~ \1\, condition_score == 2 ~\2\,condition_score == 3 ~ \3\, condition_score == 4 ~\4\,condition_score == 5 ~ \5\, condition_score == 6 ~\6\,condition_score == 7 ~ \7\, condition_score == 8 ~\8\, condition_score ==9 ~\9\, TRUE ~ as.character(condition_score))) %>%
group_by(site, month, condition_score_bin) %>% dplyr ::summarise(Count= n()) %>%
ungroup() %>%
mutate(Proportion = Count/sum(Count))
df_BCS_proportions<- na.omit(df_BCS_proportions)
df_BCS_proportions$month <- factor(df_BCS_proportions$month, levels = c(\5\,\6\,\7\, \8\, \9\, \10\, \11\),
labels=c(\May\, \June\, \July\, \Aug\, \Sept\, \Oct\, \Nov\))
df_BCS_proportions$site <- factor(df_BCS_proportions$site, levels = c(\ASHC\,\FENC\,\GOLD\, \LAUR\),
labels=c(\Ash Creek\, \Fence Creek\, \Gold Star\, \Laurel Hollow\))
bcs.prop.2023 <- ggplot(data=df_BCS_proportions, aes(x=month, y= Proportion, fill=condition_score_bin)) +
geom_bar(width = .5, stat=\identity\, position = \fill\, colour = \black\)+
theme_bw() + theme(panel.grid.minor = element_blank())+
theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1, size = rel(.9)))+
theme(panel.grid.major.x =element_blank())+
labs(title=\Body condition scores in 2023\, x =\Month\, y = \Proportion of body condition scores \)+ theme(axis.title.y = element_text(size = rel(1.2), angle =90), axis.title.x = element_text(size = rel(1.2), angle = 0))+ scale_fill_brewer(palette = \Blues\) +
theme(strip.text = element_text(size = 15))+
theme (legend.title = element_text(size = 18))+
theme(title = element_text(size = 17))+
theme(axis.text=element_text(size=17))+
labs(fill =\Body Condition Score\)+
facet_wrap(~ site )
bcs.prop.2023
#pdf(paste0(path = \Lab_Data_TissueProcessing/output\ ,\/BCS_proportion_2023.pdf\), height = 7, width = 13)
#print(bcs.prop.2023)
#dev.off()
#BCS_proportion_all+scale_fill_manual(values = c(\#003C30\,\#01665E\,\#80CDC1\,\#C7EAE5\,\#F6E8C3\,\#DFC27D\,\#BF812D\, \#8C510A\,\#543005\ ))
#scale_fill_manual(values = c(\#003C30\,\#01665E\,\#80CDC1\,\#C7EAE5\,\azure1\,\slategray1\,\slategray3\, \slategray4\, \gray25\ ))
f <- function(pal) brewer.pal(brewer.pal.info[pal, \maxcolors\], pal)
(cols <- f(\YlGnBu\))
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only 2023 data\ndata_2023 <- data_all%>%  filter(!year==\\2024\\)\n\ndf_BCS_proportions<- data_2023 %>%\n  mutate(condition_score_numeric = as.numeric(condition_score),condition_score_bin = case_when(condition_score == 1 ~ \\1\\, condition_score == 2 ~\\2\\,condition_score == 3 ~ \\3\\, condition_score == 4 ~\\4\\,condition_score == 5 ~ \\5\\, condition_score == 6 ~\\6\\,condition_score == 7 ~ \\7\\, condition_score == 8 ~\\8\\, condition_score ==9 ~\\9\\, TRUE ~ as.character(condition_score))) %>%\n  group_by(site, month, condition_score_bin) %>% dplyr ::summarise(Count= n()) %>%\n  ungroup() %>%\n  mutate(Proportion = Count/sum(Count))\n\ndf_BCS_proportions<- na.omit(df_BCS_proportions)\n\ndf_BCS_proportions$month <- factor(df_BCS_proportions$month, levels = c(\\5\\,\\6\\,\\7\\, \\8\\, \\9\\, \\10\\, \\11\\),\n        labels=c(\\May\\, \\June\\, \\July\\, \\Aug\\, \\Sept\\, \\Oct\\, \\Nov\\))\ndf_BCS_proportions$site <- factor(df_BCS_proportions$site, levels = c(\\ASHC\\,\\FENC\\,\\GOLD\\, \\LAUR\\),\n        labels=c(\\Ash Creek\\, \\Fence Creek\\, \\Gold Star\\, \\Laurel Hollow\\))\n\nbcs.prop.2023 <- ggplot(data=df_BCS_proportions, aes(x=month, y= Proportion, fill=condition_score_bin)) +\n  geom_bar(width = .5, stat=\\identity\\, position = \\fill\\, colour = \\black\\)+  \n   theme_bw() +  theme(panel.grid.minor = element_blank())+ \n  theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1, size = rel(.9)))+\n  theme(panel.grid.major.x =element_blank())+\n  labs(title=\\Body condition scores in 2023\\, x =\\Month\\, y = \\Proportion of body condition scores \\)+ theme(axis.title.y = element_text(size = rel(1.2), angle =90), axis.title.x = element_text(size = rel(1.2), angle = 0))+ scale_fill_brewer(palette = \\Blues\\) +\n  theme(strip.text = element_text(size = 15))+\n  theme (legend.title = element_text(size = 18))+\n  theme(title = element_text(size = 17))+\n  theme(axis.text=element_text(size=17))+\n  labs(fill =\\Body Condition Score\\)+\n  facet_wrap(~ site )\nbcs.prop.2023\n\n#pdf(paste0(path = \\Lab_Data_TissueProcessing/output\\ ,\\/BCS_proportion_2023.pdf\\), height = 7, width = 13)\n#print(bcs.prop.2023)\n#dev.off()\n\n#BCS_proportion_all+scale_fill_manual(values = c(\\#003C30\\,\\#01665E\\,\\#80CDC1\\,\\#C7EAE5\\,\\#F6E8C3\\,\\#DFC27D\\,\\#BF812D\\, \\#8C510A\\,\\#543005\\ ))\n#scale_fill_manual(values = c(\\#003C30\\,\\#01665E\\,\\#80CDC1\\,\\#C7EAE5\\,\\azure1\\,\\slategray1\\,\\slategray3\\, \\slategray4\\, \\gray25\\ )) \n\nf <- function(pal) brewer.pal(brewer.pal.info[pal, \\maxcolors\\], pal)\n(cols <- f(\\YlGnBu\\))\n```\n```\n\n<!-- rnb-source-end -->\n"} -->
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```r
```r
#Coding graphs for LIS Conference - only 2023 data
data_2023 <- data_all%>% filter(!year==\2024\)
df_BCS_proportions<- data_2023 %>%
mutate(condition_score_numeric = as.numeric(condition_score),condition_score_bin = case_when(condition_score == 1 ~ \1\, condition_score == 2 ~\2\,condition_score == 3 ~ \3\, condition_score == 4 ~\4\,condition_score == 5 ~ \5\, condition_score == 6 ~\6\,condition_score == 7 ~ \7\, condition_score == 8 ~\8\, condition_score ==9 ~\9\, TRUE ~ as.character(condition_score))) %>%
group_by(site, month, condition_score_bin) %>% dplyr ::summarise(Count= n()) %>%
ungroup() %>%
mutate(Proportion = Count/sum(Count))
df_BCS_proportions<- na.omit(df_BCS_proportions)
df_BCS_proportions$month <- factor(df_BCS_proportions$month, levels = c(\5\,\6\,\7\, \8\, \9\, \10\, \11\),
labels=c(\May\, \June\, \July\, \Aug\, \Sept\, \Oct\, \Nov\))
df_BCS_proportions$site <- factor(df_BCS_proportions$site, levels = c(\ASHC\,\FENC\,\GOLD\, \LAUR\),
labels=c(\Ash Creek\, \Fence Creek\, \Gold Star\, \Laurel Hollow\))
bcs.prop.2023 <- ggplot(data=df_BCS_proportions, aes(x=month, y= Proportion, fill=condition_score_bin)) +
geom_bar(width = .5, stat=\identity\, position = \fill\, colour = \black\)+
theme_bw() + theme(panel.grid.minor = element_blank())+
theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1, size = rel(.9)))+
theme(panel.grid.major.x =element_blank())+
labs(title=\Body condition scores in 2023\, x =\Month\, y = \Proportion of body condition scores \)+ theme(axis.title.y = element_text(size = rel(1.2), angle =90), axis.title.x = element_text(size = rel(1.2), angle = 0))+ scale_fill_brewer(palette = \Blues\) +
theme(strip.text = element_text(size = 15))+
theme (legend.title = element_text(size = 18))+
theme(title = element_text(size = 17))+
theme(axis.text=element_text(size=17))+
labs(fill =\Body Condition Score\)+
facet_wrap(~ site )
bcs.prop.2023
#pdf(paste0(path = \Lab_Data_TissueProcessing/output\ ,\/BCS_proportion_2023.pdf\), height = 7, width = 13)
#print(bcs.prop.2023)
#dev.off()
#BCS_proportion_all+scale_fill_manual(values = c(\#003C30\,\#01665E\,\#80CDC1\,\#C7EAE5\,\#F6E8C3\,\#DFC27D\,\#BF812D\, \#8C510A\,\#543005\ ))
#scale_fill_manual(values = c(\#003C30\,\#01665E\,\#80CDC1\,\#C7EAE5\,\azure1\,\slategray1\,\slategray3\, \slategray4\, \gray25\ ))
f <- function(pal) brewer.pal(brewer.pal.info[pal, \maxcolors\], pal)
(cols <- f(\YlGnBu\))
```
```
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#Coding graphs for LIS Conference - only 2023 data (continued)
df_3_prop<- select(data_2023, -c(\site\))
#Count and proportion table for 2023 bcs scores by month
bcs_table <- table(data_2023$condition_score, data_2023$month, data_2023$site)
names(dimnames(bcs_table)) <- c(\Body Condition Score\, \Month\, \Site\)
bcs_table <- addmargins(bcs_table)
bcs_table
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```r
```r
#Coding graphs for LIS Conference - only 2023 data (continued)
df_3_prop<- select(data_2023, -c(\site\))
#Count and proportion table for 2023 bcs scores by month
bcs_table <- table(data_2023$condition_score, data_2023$month, data_2023$site)
names(dimnames(bcs_table)) <- c(\Body Condition Score\, \Month\, \Site\)
bcs_table <- addmargins(bcs_table)
bcs_table
```
```
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sessionInfo()
````
```r
sessionInfo()
```
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